Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Blood
Cell type
MUTZ-3
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous

Attributes by original data submitter

Sample

source_name
MUTZ-3
cell line
MUTZ-3
cell type
Acute myelomonocytic leukemia
chip antibody
CTCF antibody (abcam, ab128873)

Sequenced DNA Library

library_name
GSM6605302
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed on chromatin from 2e6 MUTZ-3 MECOM and AAVS1 edited cells after magnetic sorting for CD34+ cells (Stemcell 17856). Sorted cells were cross-linked with 1% methanol-free formaldehyde (Pierce Life Technologies, 28906), quenched with 0.125 M glycine and frozen at -80 °C and stored until further processing. ChIP reaction was performed with iDeal ChIP-seq kit for Transcription Factors (Diagenode, C01010055) with modifications of the manual detailed below. Lysed samples were sonicated using the E220 sonicator (Covaris, 500239) in microTUBE AFA Fiber Pre-Slit Snap-Cap tubes (Covaris, 520045) with settings for 200bp DNA shearing. Sheared chromatin was immunoprecipitated with 2.5μg CTCF antibody (abcam, ab128873, RRID:AB_11144295) or 2.5μg IgG antibody (Diagenode, C15410206, RRID: AB_2722554). Eluted and decross-linked DNA was purified with MicroChIP DiaPure columns (Diagenode, C03040001) and eluted in 30μL of NucleaseFree water. ChIP and input libraries for sequencing were prepared with ThruPLEX® DNA-Seq Kit (Takara, R400674) and DNA Single Index Kit - 12S Set A (Takara, R400695). Size selection steps were performed with Magbio Genomics Inc HighPrep PCR beads (Fisher Scientific, 50-165-6582). Subsequently, ChIP-seq library was quantified with Agilent Bioanalyzer. The libraries were sequenced at Broad Institute Genomic Services by using the Illumina NextSeq 500 platform and the 150-bp paired-end configuration to obtain at least 30 million reads per sample.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
56503786
Reads aligned (%)
97.2
Duplicates removed (%)
16.3
Number of peaks
76303 (qval < 1E-05)

hg19

Number of total reads
56503786
Reads aligned (%)
96.7
Duplicates removed (%)
16.7
Number of peaks
76664 (qval < 1E-05)

Base call quality data from DBCLS SRA